See also
OTU / denoising pipeline
Alpha diversity
Beta diversity
Microbial taxonomy
Rarefaction
Which taxonomy database should I use?
Interpreting diversity metrics
Recommended alpha and beta metrics
Comparing alpha diversity between groups
Statistical significance of diversity differences
Diversity analysis investigates questions such as "how many species are in a sample?" and "how similar are these two samples?". The diversity in a single sample is called alpha diversity, and the diversity (differences or similarities) between two samples is called beta diversity.
The input data used for diversity analysis is an OTU table. A tree for the OTUs is also needed for UniFrac beta diversity analysis, this can be created using the cluster_agg command.
Usearch supports diversity analysis through the alpha_div, alpha_div_rare and beta_div commands. These commands support several popular diversity metrics.
You can visualize diversity using octave plots.
Note that most standard diversity metrics are difficult to interpret or invalid for NGS OTUs.
You can test for
statistically significant
differences in alpha diversity between groups by using the
alpha_div_sig command.
Taxonomy for the OTU sequences can be predicted using the sintax command. See also Which taxonomy database should I use?
A tree for the OTU sequences can be generated using the
cluster_aggd command.